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  Anti-il-13 antibodies and complexesUSPTO Application #: 20070048785Title: Anti-il-13 antibodies and complexes Abstract: Anti-IL-13 antibodies, crystals of anti-IL-13 antibodies, IL-13 polypeptide/anti-IL-13 antibody complexes, crystals of IL-13 polypeptide/anti-IL-13 antibody complexes, IL-13Rα1 polypeptide/IL-13 polypeptide/anti-IL-13 antibody complexes, crystals of IL-13Rα1 polypeptide/IL-13 polypeptide/anti-IL-13 antibody complexes, and related methods and software systems are disclosed. (end of abstract) Agent: Fish & Richardson P.C. - Minneapolis, MN, US Inventors: Laura Long Lin, Kevin D. Parris, Amy Sze Pui Tam, Xiang-Yang Tan, Tania Shane, John Dumas, James M. Wilhelm, Mark Stahl, Lidia Mosyak, Zhixiang Hu USPTO Applicaton #: 20070048785 - Class: 435007100 (USPTO) Related Patent Categories: Chemistry: Molecular Biology And Microbiology, Measuring Or Testing Process Involving Enzymes Or Micro-organisms; Composition Or Test Strip Therefore; Processes Of Forming Such Composition Or Test Strip, Involving Antigen-antibody Binding, Specific Binding Protein Assay Or Specific Ligand-receptor Binding Assay The Patent Description & Claims data below is from USPTO Patent Application 20070048785. Brief Patent Description - Full Patent Description - Patent Application Claims
RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application No. 60/578,736, filed Jun. 9, 2004, U.S. Provisional Patent Application No. 60/578,473, filed Jun. 9, 2004, and U.S. Provisional Patent Application No. 60/581,375 filed Jun. 22, 2004. The contents of each of these applications are incorporated herein by reference in their entirety. TECHNICAL FIELD [0002] The invention relates to anti-IL-13 antibodies, crystals of anti-IL-13 antibodies, IL-13 polypeptide/anti-IL-13 antibody complexes, crystals of IL-13 polypeptide/anti-IL-13 antibody complexes, IL-13R.alpha.1 polypeptide/IL-13 polypeptide/anti-IL-13 antibody complexes, crystals of IL-13R.alpha. 1 polypeptide/IL-13 polypeptide/anti-IL-13 antibody complexes, and related methods and software systems. BACKGROUND [0003] Interleukin-13 (IL-13) is a pleiotropic cytokine involved in immune response conditions, such as atopy, asthma, allergy, and inflammatory response. The role of IL-13 in immune response is facilitated by its effect on cell-signaling pathways. For example, IL-13 can promote B cell proliferation, induce B cells to produce IgE, and down regulate the production of proinflammatory cytokines. IL-13 can also increase expression of VCAM-1 on endothelial cells, and enhance expression of class II MHC antigens and various adhesion molecules on monocytes. [0004] IL-13 function is mediated through an interaction with its receptor on hematopoietic and other cell types. The human IL-13 receptor (IL-13R) is a heterodimer that includes the interleukin-4 receptor .alpha. chain, IL-4R.alpha., and the IL-13 binding chain, IL-13R.alpha.1. The association of IL-13 with its receptor induces the activation of STAT6 (signal transducer and activation of transcription 6) and JAK1 (Janus-family kinase) through a binding interaction with the IL-4R.alpha. chain. IL-13R.alpha.2, which may be found on the cell surface or in soluble form in the circulation, binds to IL-13 with high affinity but does not mediate cellular responses to IL-13. It is thought to function as a decoy receptor. SUMMARY [0005] In one aspect, the invention features a crystalline antibody. The crystalline antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody. [0006] In another aspect, the invention features a crystalline composition that includes an antibody. The antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody. [0007] In a further aspect, the invention features a crystalline complex that includes an IL-13 polypeptide and an antibody. The antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody. [0008] In another aspect, the invention features a crystalline complex that includes an IL-13R.alpha.1 polypeptide and an IL-13 polypeptide. [0009] In yet another aspect, the invention features a method that includes using a three-dimensional model of an antibody to design an agent that interacts with an IL-13 polypeptide. The antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody. [0010] In another aspect, the invention features a method that includes using a three-dimensional model of an IL-13 polypeptide to design an agent that interacts with the IL-13 polypeptide. [0011] In another aspect, the invention features a method that includes using a three-dimensional model of an IL-13 polypeptide bound to an IL-13R.alpha.1 polypeptide to design an agent that interacts with the IL-13 polypeptide. [0012] In another aspect, the invention features a method that includes selecting an agent by performing rational drug design with a three-dimensional structure of a crystalline complex that includes an IL-13 polypeptide; contacting the agent with an IL-13 polypeptide; and detecting the ability of the agent to bind the IL-13 polypeptide. [0013] In a further aspect, the invention features a method that includes contacting an IL-13 polypeptide with an antibody to form a composition; and crystallizing the composition to form a crystalline complex in which the antibody is bound to the IL-13 polypeptide. The antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody, and the crystalline complex can diffract X-rays to a resolution of at least about 3.5 .ANG.. [0014] In another aspect, the invention features a method that includes contacting an IL-13 polypeptide with an antibody and an IL-13R.alpha.1 polypeptide to form a composition, and crystallizing the composition to form a crystalline complex in which the antibody and the IL-13R.alpha.1 polypeptide are each bound to the IL-13 polypeptide. The antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody, and the crystalline complex can diffract X-rays to a resolution of at least about 3.5 .ANG.. [0015] In another aspect, the invention features a software system that includes instructions for causing a computer system to accept information relating to a structure of an IL-13 polypeptide bound to an antibody, the antibody including an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody. The instructions also cause the computer system to accept information relating to a candidate agent and to determine binding characteristics of the candidate agent to the IL-13 polypeptide. The determination of binding characteristics is based on the information relating to the structure of the IL-13 polypeptide and the information relating to the candidate agent. [0016] In another aspect, the invention features a computer program residing on a computer readable medium. A plurality of instructions is stored on the computer readable medium. When the instructions are executed by one or more processors, the one or more processors will accept information relating to a structure of an IL-13 polypeptide bound to an antibody, the antibody being an anti-IL-13 polypeptide or a Fab fragment of an anti-IL-13 antibody; accept information relating to a candidate agent; and determine binding characteristics of the candidate agent to the IL-13 polypeptide. Determination of the binding characteristics is based on the information relating to the structure of the IL-13 polypeptide and the information relating to the candidate agent. [0017] In another aspect, the invention features a method that includes accepting information relating to the structure of an IL-13 polypeptide bound to an antibody and modeling the binding characteristics of the IL-13 polypeptide with a candidate agent. The antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody. The method of accepting information and modeling the binding characteristics is implemented by a software system. [0018] In another aspect, the invention features a computer program residing on a computer readable medium containing a plurality of instructions. When the instructions are executed by one or more processors, the one or more processors will accept information relating to the structure of an IL-13 polypeptide bound to an antibody, the antibody being an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody; and model the binding characteristics of the IL-13 polypeptide with a candidate agent. [0019] In another aspect, the invention features a software system, that includes instructions for causing a computer system to accept information relating to the structure of an IL-13 polypeptide bound to an antibody, and model the binding characteristics of the IL-13 polypeptide with a candidate agent. The antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody. [0020] In another aspect, the invention features a crystalline antibody. The antibody is capable of binding to a site of an IL-13 polypeptide to which an IL-4R polypeptide binds in vivo. Continue reading... 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